Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms

Abstract

Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

“…Such enzymes include malic enzyme (ME), pyruvate carboxylase (PC), phospho enol pyruvate carboxykinase (PEPCK), and phosphoenolpyruvate carboxylase (PEPC), together referred to as the pyruvate hub [91,105]. Though these enzymes likely have important roles in cellular metabolism, though their specific functions remain largely unknown [90–91,105–108]. Most of the genes in the mitochondrial pyruvate hub are strongly upregulated in the dark, consistent with enhanced processing of 3C/4C skeletons during this phase (Fig 7).…”

“…Further, this model highlights the degree to which the chloroplast and mitochondria are metabolically and energetically connected, and able to communicate their metabolic status through the dynamic exchange of carbon skeletons and nitrogen groups. Despite the essential roles of transporters in regulating pathway connectivity and intracellular metabolite fluxes, these transporters remain conspicuously absent from this and many models of diatom metabolism [90–92,108,120]. In the P .…”

Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatomPhaeodactylum tricornutum

“…The transcript abundance of GOX_m was 40 times higher than GOX_x on average, and GOX_m was coexpressed with known photorespiration genes, including glycine decarboxylase and phosphoglycolate phosphatase (Figs , S8). Taken together, the flux predictions are consistent with biochemical evidence (Schmitz et al ., ), gene expression in P. tricornutum (Smith et al ., ) and the centric diatom T. pseudonana (Davis et al ., ).…”

“…In plants, 2‐phosphoglycolate is recovered as glycerate through a series of metabolic reactions in the peroxisome and mitochondria, although this process is considered wasteful as it occurs at the expense of energy and fixed carbon (C; Wingler et al ., ). In P. tricornutum , open questions remain regarding how photorespiration intersects with the broader metabolic network (Davis et al ., ). Thus, the role of these metabolic pathways to facilitate photoprotection and cross‐compartment energy coupling has not been fully explored.…”

Optimizing photorespiration for improved crop productivity

“…This information can then be used in engineering approaches. For example, the peroxisomal glyoxylate cycle could convert glyoxylate to malate, as opposed to glycine, as a photorespiratory intermediate, which is proposed from in silico analysis and select in vivo results (Davis et al ). Different environmental pressures may have also induced evolutionary changes to photorespiration that may be elucidated by expanding genomic data and could drive changes in engineering strategies.…”